This question has been asked a LOT of times, and is written left and right :

After you have saved in-game, just press L+R+A+Select to "commit" the save, and copy its contents to the MicroSD card. It is the only way to keep your saves, besides QPC which shouldn't really be needed anyways.

From Fifthelement's guide (should give it a read, really clear on the supercard operations):

Normal GBA Save:

If you would like to make a normal GBA game save as if you were using a real GBA gamecart you’ll need to follow these instructions: Play your GBA game until you come upon a checkpoint or save spot. Once you reach the save spot you’ll need to manually save the game unless it automatically does so. Once you are sure the game has been saved internally, to the SuperCard SRAM, you’ll need to press Left Trigger, Right Trigger, Select, and A buttons simultaneously to finalize the save. Once you use the button combination above another small menu will appear and you’ll need to select "Save" and press the A button and then select "Yes" while pressing the A button once more. This will now bring up a counter which will show your save progress as the save is transferred to your flash media.

You’ll need to use this save method each time for saving or else your games will not be saved into memory. On a positive note, when using this option you do not have to load your game again when you restart your DS as your last save game will be preloaded into the save game slot of the GBA game you are playing just as a normal GBA gamecart does.

Real Time Save:

If you would like to save your game anywhere while playing and be able to restart your game anywhere you’ll need to follow these instructions:

Play your GBA game until you want to stop playing and save the game. Once you are ready to save you’ll need to press Left Trigger, Right Trigger, Select, and B buttons simultaneously to finalize the save. Once you use the button combination above another small menu will appear and you’ll need to select "Save" and press the A button and then select "Yes" while pressing the A button once more. This will now bring up a counter which will show your save progress as the save is transferred to your flash media.

To load a Real Time Save you’ll need to use the same button combination as above but select the “Load” option instead of “Save”. Follow the menu instructions and your save will be loaded back to the exact point that you left off from. This method will have to be used each time you save and load a game and if you fail to do so you will lose the data up your last save progress.

Saving normally in GBA games in which the Normal & Real Time Save functions are not available:

You may find some games which will refuse to work when "Enble Restart”, “Enable saver Patch” and “Enable Real Time Save” are checked so you’ll need to save the game manually by following these instructions:

Play your GBA game until you come upon a checkpoint or save spot. Once you reach the save spot you’ll need to manually save the game unless it automatically does so. Once you are sure the game has been saved internally, to the SuperCard SRAM, you’ll need to quickly turn your DS off then on again (power-cycle it). If the GBA ROM is able to be patched with the "Enble Restart” but not the other two save options return to the SuperCard menu by pressing Left Trigger, Right Trigger, Select, and Start buttons simultaneously. Now once back in the SuperCard menu press right on the digital-pad so that you are under the "Saver" menu tab. Next find the “SAV” file associated with your ROM and select it by pressing the A button and finally press it again when prompted to save. Your GBA save game will now be manually saved to your flash media and should load automatically, just as a normal GBA save, next time you restart your DS.